tbuckley/cabot-search huggingface dataset:
Abstract 1350: The role of phosphatidylserine scramblases in tumor progression
Authors: Varsha Gadiyar, Viralkumar Davra, David Calianese, Kevin Lahey, Raymond B. Birge
Journal: Cancer Research (2022)

Abstract Introduction: Phosphatidylserine (PS), an anionic phospholipid, is asymmetrically distributed in the inner leaflet of the phospholipid bilayer in normal cells under homeostasis. However, PS is constitutively externalized in the tumor microenvironment (TME); on viable cells that undergo stress, such as hypoxic tumor cells, stressed tumor vascular endothelial cells, as well as on cells undergoing apoptosis. This high PS harbors a pro-tumorigenic micro-environment, as myeloid cells expressing PS receptors (Mertk, Tyro3 and Axl) engage with externalized PS and secrete immunosuppressive cytokines. PS is externalized on viable cells by a calcium activated scramblase TMEM16F and on apoptotic cells by a caspase activated scramblase called Xkr8. Here, to study the mechanisms by which PS is externalized in the TME, we hypothesize that TMEM16F and Xkr8 are the major scramblases responsible for creating an immune suppressive milieu in the tumor microenvironment. Methods: To study the mechanisms of PS dysregulation in the tumor microenvironment, TMEM16F and Xkr8 were knocked out in E0771 murine breast cancer cell line using CRISPR/Cas9. The knockouts were validated by western blotting, q-RT-PCR and surveyor assays. Results: TMEM16F KO E0771 cells express lower basal levels of PS compared to WT E0771 cells when detected by Annexin V staining by flow cytometry. TMEM16F KO cells are also less responsive to activation by calcium ionophore. TMEM16F KO, Xkr8 KO and WT E0771 cells have similar viability and migration patterns in response to Gas6, indicating that the cells themselves do not have altered oncogenic potential. TMEM16F KO E0771 cells injected into the inguinal mammary gland fat pad of C57BL6 syngeneic mice showed modest but significantly reduced tumor growth compared to the E0771 WT tumors, suggesting that TMEM16F mediated PS externalization could play a role in exacerbating tumor progression. Conclusion: TMEM16F driven PS externalization contributes to tumor growth. The effect of TMEM16F KO on immune regulation of the tumor milieu will be discussed. These data corroborate previous studies targeting PS in tumors therapeutically using anti-PS antibodies and suggests a role for scramblases in pleiotropic immune-suppression in the tumor. Citation Format: Varsha Gadiyar, Viralkumar Davra, David Calianese, Kevin Lahey, Raymond B. Birge. The role of phosphatidylserine scramblases in tumor progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1350.
Abstract 1719: Investigating intra-tumor heterogeneity using multiplexed immunohistochemistry &amp; deep learning: A new approach to spatially map the tumor microenvironment
Authors: Kouther Noureddine, Paul Gallagher, Martial Guillaud, Calum MacAulay
Journal: Cancer Research (2022)

Abstract The tumor microenvironment (TME) is a highly complex mixture containing epithelium, stroma and a diverse network of immune cells &amp; the spatial organization of these immune cells within the TME reflects a crucial process in anti-tumor immunity. At present, the usual standard of care for assessing if a patient has cancer, its stage and its likely future biological behaviour is visual examination of one or more stained sections. Although recent advances in multiple immunostaining have enabled characterization of several parameters on a single tissue section. For a higher dimensional chromogen based methodology, we have developed a multiplexed IHC (mIHC) procedure combining multiple labels per round with several sequential rounds, enabling analysis of complex immune cell populations on a single slide through consecutive cycles of staining, destaining &amp; hyperspectral imaging. By integrating serial imaging, sequential labeling &amp; image registration, we are able to spatially map the TME. The process presented is using absorption microscopy, enabling these images to be done in a reasonable time frame. Robust, accurate, segmentation of cell nuclei for overlapping nuclei is one of the most significant unsolved issues in digital pathology. Using the counterstain concentration images from our mIHC methodology, we have trained a deep learning segmentation method to accurately segment individual cell nuclei within overlapping clusters of nuclei. By combining a multiplexed IHC technique which enables the detection of multiple markers on a single slide with deep learning segmentation methods to segment every individual cell nuclei in tissue sections with an accuracy comparable to human annotation. We can analyze the cell-cell interactions between immune and tumour cells, enhancing our ability to perform molecularly based single cell analysis of multiple cell types simultaneously within the tissue. These two techniques joined can be scaled up to the entire tissue section level, improving our understanding of the biological aggressiveness of specific cancers &amp; enabling an accurate spatial cell level representation of the tissue. Citation Format: Kouther Noureddine, Paul Gallagher, Martial Guillaud, Calum MacAulay. Investigating intra-tumor heterogeneity using multiplexed immunohistochemistry &amp; deep learning: A new approach to spatially map the tumor microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1719.
Abstract 1180: Discovery of CC-91516, a potent and selective ERK/NLK inhibitor, with anti-tumor activity in preclinical cancer models harboring BRAF or CTNNB1 mutation
Authors: Shuichan Xu, Tam Tran, Dan Zhu, Tao Shi, David Mikolon, Jim Leisten, Philip Chamberlain, Laurie LeBrun, Sogole Bahmanyar, Ning Jiang, Jingjing Zhao, Mehnaz Malek, Ellen Filvaroff, Heather Raymon, Robert Hubbard, John Boylan
Journal: Cancer Research (2022)

Abstract CC-91516 (also called CC0776314), a selective and potent inhibitor of ERK1/2 and NLK, was discovered via a phenotypic screen of a kinase-focused library for compounds that synergize with mTOR kinase inhibitor CC-223 to induce apoptosis in combination with CC-223. Broad kinase selectivity profiling identified ERK1/2 and NLK as targets of CC-91516. Crystal structure of CC-91516 in complex with ERK2 reveals that its 2, 4, 6-trichlorophenyl moiety binds to a unique back pocket of the adenosine-5′-triphosphate (ATP) binding site of ERK2, which is not accessible to other ERK inhibitors such as BVD-523 and GDC-0994. This unique binding mode of CC-91516 leads to a slow off-rate for its ERK binding with long residence time disrupting both the active and inactive ERK forms. Consequentially, CC-91516 causes sustained inhibition of the MAPK pathway in BRAF mutant colorectal cancer cells. In addition, CC-91516 also regulates Wnt/β-catenin and YAP pathways in multiple cancer cell lines. CC-91516 shows potent yet selective anti-proliferative activity against a large panel of cancer cell lines. Activating mutations in BRAF or CTNNB1 gene associate with sensitivity to CC-91516-mediated anti-proliferative activity while mutations in RB and PI3K/PTEN pathway associate with resistance. CC-91516 inhibits ex vivo colony formation of PDX models with BRAF and CTNNB1 mutations. In addition, CC-91516 potently induces apoptosis, inhibits survival, and overcomes resistance to MEK inhibitor trametinib of BRAF or CTNNB1 mutant cancer cells in long-term culture assay in vitro. CC-91516 has good oral bioavailability and shows excellent anti-tumor activity in vivo against both BRAF and CTNNB1 mutant xenograft models. DMPK and toxicology studies showed robust oral exposure across preclinical species. In summary, CC-91516 has demonstrated preclinical anti-tumor activities and DMPK and safety profiles in support of its clinical development. Citation Format: Shuichan Xu, Tam Tran, Dan Zhu, Tao Shi, David Mikolon, Jim Leisten, Philip Chamberlain, Laurie LeBrun, Sogole Bahmanyar, Ning Jiang, Jingjing Zhao, Mehnaz Malek, Ellen Filvaroff, Heather Raymon, Robert Hubbard, John Boylan. Discovery of CC-91516, a potent and selective ERK/NLK inhibitor, with anti-tumor activity in preclinical cancer models harboring BRAF or CTNNB1 mutation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1180.
Abstract 1301: T cell intrinsic androgen receptor activity regulates response to immunotherapy
Authors: Amy E. Moran, Fanny Polesso, Zheng Xia, George Thomas, Julie Graff
Journal: Cancer Research (2022)

Abstract Immune checkpoint blockade has revolutionized the field of oncology inducing durable anti-tumor immunity in many solid tumors. In advanced prostate cancer patients, immunotherapy treatments have largely failed. Androgens have pleiotropic functions in prostate cancer; they are potent drivers of cancer cell growth and can suppress T cell function. In metastatic prostate cancer, intratumor androgen levels can remain high. Androgen deprivation therapy, the backbone of clinical care in prostate cancer, is classically administered to inhibit tumor cell growth. We postulated that this therapy also impacts tumor associated T cells. To test this hypothesis, we performed transcriptome profiling of individual leukocytes isolated from metastatic prostate cancer lesions resistant to androgen deprivation therapy (ADT) and androgen receptor (AR) antagonism and prior to treatment with a PD-1 inhibitor. We reveal that inhibition of AR activity in CD8 T cells prevented T cell exhaustion and improved responsiveness to PD-1 targeted therapy via increased IFNγ expression. Notably, AR directly bound to Ifng and eviction of this transcription factor with a small molecule significantly increased cytokine production in CD8 T cells. Furthermore, genomic deletion of Ar prevented chronically stimulated CD8 T cells from losing their ability to make IFNγ upon restimulation. Finally, we demonstrate that AR blockade sensitizes multiple tumor mouse models to effective checkpoint blockade by directly enhancing CD8 T cell function. Together, our findings establish T cell specific AR activity as one mechanism of immunotherapy resistance and show that targeting AR can improve immunotherapy outcomes. Citation Format: Amy E. Moran, Fanny Polesso, Zheng Xia, George Thomas, Julie Graff. T cell intrinsic androgen receptor activity regulates response to immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1301.
The Keloid Area and Severity Index (KASI): an objective tool for the evaluation of keloids
Authors: Emily E. Limmer, Eva Kerby, Shelby Lies, Byron Limmer, Rachel Limmer, Noelle Teske, Stephanie Savory, Joan S. Reisch, Donald A. Glass
Journal: British Journal of Dermatology (2022)

To aid in the standardization of evaluating patients with multiple keloids, a Keloid Area and Severity Index (KASI) was developed using patient feedback, previous literature, and clinical expertise. The system was validated using intrarater and interrater reliability assessments. Here, we present a verified, reliable method of assessing keloid area and severity in clinical and research settings.
Abstract 1085: PRO1184, a novel folate receptor alpha-directed antibody-drug conjugate, demonstrates robust anti-tumor activity in mouse carcinoma models
Authors: Baiteng Zhao, Lei Wang, Haidong Liu, Suping Huang, Xiao Shang, Tae Han
Journal: Cancer Research (2022)

Abstract PRO1184 is an antibody-drug conjugate (ADC) directed toward folate receptor alpha (FOLR1), a glycosyl phosphatidylinositol anchored membrane protein. FOLR1 is overexpressed in many cancers with unmet medical need, including ovarian, lung, and breast cancers, while normal tissue expression is limited. PRO1184 is comprised of a 1) human monoclonal antibody that selectively binds to FOLR1, 2) a cleavable, hydrophilic linker, and 3) exatecan, a topoisomerase 1 inhibitor. Upon binding to FOLR1 on the surface of malignant cells, PRO1184 is internalized and exatecan released through enzymatic cleavage of the linker. Exatecan blocks the ligation step of the cell cycle and generates DNA single- and double-strand breaks, which leads to cell death. The mechanism of action and clinical potential of PRO1184 was tested in a series of studies. PRO1184 bound selectively and specifically to FOLR1 with nM affinity. PRO1184 was efficiently internalized and demonstrated cytotoxicity against multiple cell lines, in vitro. In mouse carcinoma models, PRO1184 demonstrated robust anti-tumor activity across multiple tumor types that represent ovarian, non-small cell lung, and breast cancer. In addition, PRO1184 was more potent with greater tumor growth inhibition than that of a DM4-conjugated ADC. PRO1184 was tolerated at the 60 mg/kg dose level in cynomolgus monkeys and the safety profile was generally more favorable than that for a DXd-based ADC. The pharmacokinetics (PK) of PRO1184 were similar to that of the unconjugated parent antibody in rats. PRO1184 has the potential for a meaningful therapeutic window to provide an appropriate benefit to risk profile for patients with FOLR1-expressing cancers. Citation Format: Baiteng Zhao, Lei Wang, Haidong Liu, Suping Huang, Xiao Shang, Tae Han. PRO1184, a novel folate receptor alpha-directed antibody-drug conjugate, demonstrates robust anti-tumor activity in mouse carcinoma models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1085.
Abstract 5032: Data driven refinement of gene signatures for enrichment analysis and cell state characterization
Authors: Alexander T. Wenzel, Pablo Tamayo, Jill P. Mesirov
Journal: Cancer Research (2022)

Abstract In the study of human disease, the use of gene expression data has been crucial to the functional characterization of changes in molecular pathway activity and for identifying targets for novel treatments. However, the interpretation of this data is often complicated by its high dimensionality and the difficulty of identifying biological signals within a list of differentially expressed genes. Gene Set Enrichment Analysis (GSEA) is a community standard method for identifying pathway enrichment in gene expression data by testing whether a set of genes whose expression would indicate the activity of a specific process or phenotype are coordinately up- or downregulated more than would be expected by chance. As GSEA relies on high quality gene sets with coordinately regulated member genes, we maintain the Molecular Signatures Database (MSigDB) which contains 9 collections of curated, annotated gene sets representing different biological pathways and processes. Over time, we have observed that some of the MSigDB gene sets, especially those that are manually curated or defined in a very specific biological context, may not provide a sensitive and specific enough co-regulation signature for their corresponding phenotype. In response, we have created a data-driven, matrix-factorization-based refinement method to build more sensitive and specific gene sets. This method incorporates large-scale datasets from multiple sources including compendia such as the Cancer Dependency Map as well as curated protein-protein interaction networks. We will present the initial results of this refinement method as well as our ongoing work which will yield a new collection of refined gene sets that will be made freely available in MSigDB for use with GSEA and many other applications. Citation Format: Alexander T. Wenzel, Pablo Tamayo, Jill P. Mesirov. Data driven refinement of gene signatures for enrichment analysis and cell state characterization [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5032.
Abstract 5492: Activity of RP7214, a novel, selective, and potent small molecule inhibitor of DHODH, in AML
Authors: Srikant Viswanadha, Satyanarayana Eleswarapu, Swaroop Vakkalanka
Journal: Cancer Research (2022)

Abstract Background: Dihydroorotate dehydrogenase (DHODH), a rate limiting enzyme in pyrimidine synthesis, is overexpressed in certain cancers and impedes tumor cell proliferation via cell cycle arrest. RP7214 is a novel and potent DHODH inhibitor that inhibited DHODH activity in enzyme and PHA induced HWB/PBMC proliferation with IC50 and EC50 values of 7.8 &amp; 2.5/0.60 nM respectively. Herein, we describe the efficacy of RP7214 as a single agent and in combination with standard of care drugs in preclinical models of AML Methods: Cell viability of AML cell lines (U937, HL-60, THP-1, and KG-1) following incubation with RP7214 as a single agent or in combination with Azacytidine or Venetolcax for 72 h was determined in an MTT-based assay. Cell surface expression of CD11b in THP-1 and human primary bone marrow AML mononuclear cells in presence of RP7214 was evaluated by flow cytometry. Apoptosis was evaluated following incubation of cell lines with compound for 48 or 72 h, subsequent staining with Annexin-V-PE and 7-AAD, and analysis by flow cytometry. Anti-tumor potential of RP7214 as single agent was tested in subcutaneous MV-4-11 human leukemia xenograft model. Results: RP7214 inhibited AML cell proliferation in all the four cell lines tested with GI50 ranging from 2.4 to 7.6 µM. Expression of the CD11b marker on THP-1 cell surface was enhanced by 40% following incubation with 5 µM compound; effect of which was reduced to 15% in the presence of 300 µM Uridine. Incubation of primary human bone marrow AML mononuclear cells with 10 µM of RP7214 increased the CD11b+ cells by &amp;gt; 15 %. Combination of 3 µM-RP7214 and 1 µM-Azacytidine inhibited cell proliferation by &amp;gt; 25% (P &amp;lt; 0.05) compared to single agents in MV-4-11 cells. Similarly, combination of 3 µM-RP7214 with 3 nM Venetoclax demonstrated 15% (P &amp;lt; 0.05) inhibition of cell growth compared to single agents in MV-4-11 cell line. RP7214 at 3, 10, and 30 mg/kg BID demonstrated significant anti-tumor activities in both tumor size and tumor weight in subcutaneous MV-4-11 human leukemia xenograft model. Conclusions: Results demonstrate the utility of RP7214 as a single agent and in combination with standard of care drugs in inducing apoptosis and promoting differentiation to fully mature cells in AML. A Phase 2a trial in AML patients is planned. Citation Format: Srikant Viswanadha, Satyanarayana Eleswarapu, Swaroop Vakkalanka. Activity of RP7214, a novel, selective, and potent small molecule inhibitor of DHODH, in AML [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5492.
Abstract 426: Development of oridonin-based proteolysis-targeting chimera (PROTAC) degraders as effective breast cancer therapeutics
Authors: Ruixia Ma, Pingyuan Wang, Junhai Xu, Jimin Xu, Doerte R. Fricke, Yu Xue, Hyejin Kim, Haiying Chen, Xi Liu, Jia Zhou, Qiang Shen
Journal: Cancer Research (2022)

Abstract Natural products provide a wealth of resources as the molecular starting point for the development of therapeutic agents, including a plethora of anticancer drugs currently in clinical use. Oridonin is a natural diterpene compound enriched in the medicinal herb Rabdosia rubescens, and its anticancer property has been extensively studied. However, the potency of oridonin against triple-negative breast cancer (TNBC) limits its potential clinical translation. Previously, we developed a class of oridonin analogues including CYD0618 and others as effective anticancer agents to inhibit tumor growth of TNBC in vitro and in vivo. Intriguingly, CYD0618 has been shown to directly bind to and inhibit STAT3 transcription factor, which is constitutively activated in the majority of human cancers. Currently there are no FDA-approved direct STAT3 inhibitors in clinical use. Based on the proteolysis-targeting chimera (PROTAC) technology, our team designed novel oridonin- and CYD0618-based PROTACs in an attempt to achieve specific STAT3 binding and protein degradation. We determined anticancer effects of oridonin- and CYD0618-PROTACs on proliferation, colony formation, and apoptosis of the TNBC cell line MDA-MB-231. We found that oridonin- and CYD0618-based PROTACs inhibited the proliferation of MDA-MB-231 cells significantly, similarly effective as the lead compound CYD0618 and much more potent than oridonin. We then examined the expression of STAT3, pSTAT3 and protein biomarkers for tumor metastasis using Western blot. STAT3 and pSTAT3 protein levels were downregulated dose- and time-dependently in MDA-MB-231 cells treated with CYD0618 and CYD0618-PROTACs, respectively. Our results demonstrate impressive effects of CYD0618-based PROTACs against TNBC cells, primarily through direct targeting of STAT3. We are in the process of further characterizing the molecular profile of CYD0618-based PROTACs by studying its interaction with STAT3 and protein degradation as well as their efficacy against TNBC tumor xenografts in vivo. Citation Format: Ruixia Ma, Pingyuan Wang, Junhai Xu, Jimin Xu, Doerte R. Fricke, Yu Xue, Hyejin Kim, Haiying Chen, Xi Liu, Jia Zhou, Qiang Shen. Development of oridonin-based proteolysis-targeting chimera (PROTAC) degraders as effective breast cancer therapeutics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 426.